<html>
    <head>
        <title>About AntND</title>
        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
        <link rel="stylesheet" type="text/css" href="/ND/desktop/impl/helpsystem/HelpStyles.css">
    </head>
    <body>

        <img src="NDIcon.png" height="130" width="166"/> <h1>AntND</h1>
        <p>This program is meant to be a help for the manual curation and visualization of metabolic models in SBML format. </p>
    <center>
        <p>
            <img src="capture.png" name="AntND"/>
        </p>
    </center>
    <p>
        This program is able to open SBML files containing a metabolic model. Given a set of compounds used as a source (they can be represented inside the 
        metabolic model as an exchange reactions with lower bound < 0), it can calculate one or more of the 
        shortest paths from the sources to an user defined compound. This resulting path or subnetwork can be visualized in the same program or exported
        as and SBML file which will be a subset of the initial one.
    </p>
    <p>
        The program can perform simple Flux Balance Analysis using the R package sybil. For that reason, the integration of this java program with R
        must be defined in the initial files (startND_Linux.sh, startND_MacOSX.command or start_Windows.bat): <br>
        You will need to correctly configure the following:
    </p>
    <ul>             
        <li>R_HOME - This is the directory where R is installed, e.g. for Windows it will be something like C:\Program Files\R\R-2.15.0
        <li>R_LIBS_USER - This is the directory in which R installs third-party packages. It's usually a subdirectory of your personal directory, e.g. for Windows it will be something like %USERPROFILE%\Documents\R\win-library\2.15. For some R installations it might the library subdirectory of %R_HOME%, e.g. %R_HOME%\library
        <li>PATH -  Append the directory that contains R's libraries. It will be a subdirectory of %R_HOME%, e.g. for 32-bit Windows it will be something like %R_HOME%\bin\i386 or for 64-bit Windows %R_HOME%\bin\x64
        <li>JRI_LIB_PATH - This is the directory where rJava has installed its JRI libraries. It will be a subdirectory of %R_LIBS_USER%, e.g. for 32-bit Windows it will be something like %R_LIBS_USER%\rJava\jri\i386 or for 64-bit Windows %R_LIBS_USER%\rJava\jri\x64
    </ul>


    <p>
        This software can modify the model by adding or removing reaction. Any change will be recorded for each model in a text file that
        will be saved during the project saving. The user is allowed to add comments or modify this file. It can be accessed by selecting the 
        model in the left part of the screen and pressing the right button of the mouse. In the menu the option "Show changes" must be selected.
    </p>
    <p>It can list all the reactions in the selected model
        or search for specific reaction and the same for the compounds. It contains a module for the comparison of two models but it only works when 
        the two models share IDs. 
    </p>
    <p>
        The different networks or SBML files can be combined in a single SBML file using the option "Combine" that appears using the right 
        button of the mouse after selecting the models you want to combine.

    </p>
    <p>
        To analyze the resulting subnetworks or the main metabolic models, the program contains several algorithm to cluster the nodes or obtain 
        specific subnetworks based on neighborhood. 
    </p>
</body>
</html>
